1IWB

Crystal structure of diol dehydratase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase

Shibata, N.Masuda, J.Morimoto, Y.Yasuoka, N.Toraya, T.

(2002) Biochemistry 41: 12607-12617


  • PubMed Abstract: 
  • Substrate binding triggers catalytic radical formation through the cobalt-carbon bond homolysis in coenzyme B12-dependent enzymes. We have determined the crystal structure of the substrate-free form of Klebsiella oxytoca diol dehydratase*cyanocobalam ...

    Substrate binding triggers catalytic radical formation through the cobalt-carbon bond homolysis in coenzyme B12-dependent enzymes. We have determined the crystal structure of the substrate-free form of Klebsiella oxytoca diol dehydratase*cyanocobalamin complex at 1.85 A resolution. The structure contains two units of the heterotrimer consisting of alpha, beta, and gamma subunits. As compared with the structure of its substrate-bound form, the beta subunits are tilted by approximately 3 degrees and cobalamin is also tilted so that pyrrole rings A and D are significantly lifted up toward the substrate-binding site, whereas pyrrole rings B and C are only slightly lifted up. The structure revealed that the potassium ion in the substrate-binding site of the substrate-free enzyme is also heptacoordinated; that is, two oxygen atoms of two water molecules coordinate to it instead of the substrate hydroxyls. A modeling study in which the structures of both the cobalamin moiety and the adenine ring of the coenzyme were superimposed onto those of the enzyme-bound cyanocobalamin and the adenine ring-binding pocket, respectively, demonstrated that the distortions of the Co-C bond in the substrate-free form are already marked but slightly smaller than those in the substrate-bound form. It was thus strongly suggested that the Co-C bond becomes largely activated (labilized) when the coenzyme binds to the apoenzyme even in the absence of substrate and undergoes homolysis through the substrate-induced conformational changes of the enzyme. Kinetic coupling of Co-C bond homolysis with hydrogen abstraction from the substrate shifts the equilibrium to dissociation.


    Organizational Affiliation

    Department of Life Science, Graduate School of Science, Himeji Institute of Technology, 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIOL DEHYDRATASE alpha chain
A, L
554Klebsiella oxytocaGene Names: pddA (pduC)
EC: 4.2.1.28
Find proteins for Q59470 (Klebsiella oxytoca)
Go to UniProtKB:  Q59470
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DIOL DEHYDRATASE beta chain
B, E
224Klebsiella oxytocaGene Names: pddB
EC: 4.2.1.28
Find proteins for Q59471 (Klebsiella oxytoca)
Go to UniProtKB:  Q59471
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DIOL DEHYDRATASE gamma chain
G, M
173Klebsiella oxytocaGene Names: pddC (pduE)
EC: 4.2.1.28
Find proteins for Q59472 (Klebsiella oxytoca)
Go to UniProtKB:  Q59472
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, L
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
B12
Query on B12

Download SDF File 
Download CCD File 
B, E
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.790α = 90.00
b = 122.400β = 90.00
c = 207.590γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SHELXL-97refinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-10-24
    Type: Non-polymer description